CASINO V2.42: a fast and easy-to-use modeling tool for scanning electron microscopy and microanalysis users

Monte Carlo simulations have been widely used by microscopists for the last few decades. In the beginning it was a tedious and slow process, requiring a high level of computer skills from users and long computational times. Recent progress in the microelectronics industry now provides researchers with affordable desktop computers with clock rates greater than 3 GHz. With this type of computing power routinely available, Monte Carlo simulation is no longer an exclusive or long (overnight) process. The aim of this paper is to present a new user-friendly simulation program based on the earlier CASINO Monte Carlo program. The intent of this software is to assist scanning electron microscope users in interpretation of imaging and microanalysis and also with more advanced procedures including electron-beam lithography. This version uses a new architecture that provides results twice as quickly. This program is freely available to the scientific community and can be downloaded from the website: (www.gel.usherb.ca/casino).     

Analytical transmission electron microscopy and electron diffraction for characterization of multiphase Ni-P-Ti surface layer on Ti-6Al-4V alloy

The microstructure, chemical and phase composition of the hard Ni‐P‐Ti layer formed on the Ti‐6Al‐4V alloy after duplex surface treatment were investigated by light microscopy, X‐ray diffraction, scanning electron microscopy and analytical/high‐resolution transmission electron microscopy. These investigations showed that the improved mechanical and tribological properties of the surface‐treated alloy were related to the presence of a multilayered microstructure containing several phases from the Ni‐Ti‐P‐Al system.     

Scanning electron microscopy as a tool for authentication of oil yielding seed

Now‐a‐days, plant species are consumed globally for various purposes and this increasing demand leads to adulteration due to gradually exploitation in natural resources. The major causes of adulteration may be confusion in nomenclature, unawareness of authentic sources, unavailability of authentic sources, color resemblances, deficiencies in collection procedures, and misidentification. This study aims to use the microscopic techniques such as scanning electron microscopy for the authentication of the oil yielding seeds of four important and traditionally used species Prunus persica, Prunus domestica, and Eruca sativa and Argemone Mexicana from their adulterants. All of these are versatile in usage. Locally, these four plants are adulterated badly and there is need to provide a criteria and a complete monograph for correct identification. This research may prove to be helpful for quality control and as well for future studies to explore other novel aspects of these plants.     

Scanning electron microscopy as a tool for authentication of biodiesel synthesis from Linum usitatissimum seed oil

Utilization of renewable and alternative energy feedstocks such as nonedible seeds oil to deal with the increasing energy crises and related ecological concerns have gained the attention of researchers. Biodiesel is an efficient and renewable substitute for diesel engine. This work investigates the potential of inexpensive nonedible seed oil of Linum usitatissimum to synthesize biodiesel using iron sulfate green nanocatalyst through the process of transesterification. Flax seed contains about 37.5% oil content estimated through Soxhlet apparatus. Light microscopy revealed that seed size varies from 3.0 to 6.0 cm in length, 2.0 to 3.3 cm in width, and 0.7 to 1.0 mm in diameter. Color of seed varied from yellow to brown. Characterization of biodiesel is performed through GC–MS and FTIR. Scanning electron microscopy was carried out to study the morphological features of seed coat. Catalyst was characterized by scanning electron microscopy, energy diffraction X-ray, and X-ray diffraction. The diffraction peaks of Fe₃O₄ green nanoparticles were found to be in 2θ values, 30.24°, 35.62°, 38.26°, 49.56°, 57.12°, and 62.78°. Fuel properties of biodiesel are also determined and compared with ASTM standards. Linum usitatissimum biodiesel has density 0.8722 (15°C kg/L), kinetic viscosity 5.45 (40°C cSt), flash point (90°C), pour point (−13°C), cloud point (−9°C), sulfur (0.0432% wt), and total acid number (0.245 mg KOH/g). It is concluded that L. usitatissimum seed oil is a highly potential source for biodiesel production to cope with the challenge of present energy demand.     

Implication of scanning electron microscopy as a tool for identification of novel,nonedible oil seeds for biodiesel production

Biodiesel is a promising, bio-based, renewable, nontoxic, environment friendly, and alternative fuel for petroleum derived fuels which helps to reduce dependency on conventional fossil fuels. In this study, six novel, nonedible seed oil producing feedstock were explored for their potential for sustainable production of biodiesel. It is very important to correctly identify oil yielding plant species. Scanning electron microscopy (SEM) was used as reliable tool for authentic identification of oil yielding seeds. Macromorphological characters of seeds were studied with light microscopy (LM). Outcomes of LM of seeds exposed distinctive variation in seed size from 16.3 to 3.2 mm in length and 12.4 to 0.9 mm in width, shape varied from oval to triangular, and color from black to light brown. Oil content of nonedible seed ranged from 25 to 30% (w/w). Free fatty acid content of seed oil varied from 0.32 to 2.5 mg KOH/g. Moreover, ultra structural study of seeds via SEM showed variation in surface sculpturing, cell arrangement, cell shape, periclinal wall shape, margins, protuberances, and anticlinal wall shape. Surface sculpturing varied from rugged, reticulate, varrucose, papillate, and striate. Periclinal wall arrangements confirmed variation from rough, wavy, raised, depressed, smooth, and elevated whereas, anticlinal walls pattern showed variation from profuse undulating, smooth, raised, grooved, deep, curved, and depressed. It was concluded that SEM could be a latent and advanced technique in unveiling hidden micromorphological characters of nonedible oil yielding seeds which delivers valuable information to researchers and indigenous people for precise and authentic identification and recognition.     

Transmission electron microscopy characterization of the erbium silicide formation process using a Pt/Er stack on a silicon-on-insulator substrate

Very thin erbium silicide layers have been used as source and drain contacts to n‐type Si in low Schottky barrier MOSFETs on silicon‐on‐insulator substrates. Erbium silicide is formed by a solid‐state reaction between the metal and silicon during annealing. The influence of annealing temperature (450 °C, 525 °C and 600 °C) on the formation of an erbium silicide layer in the Pt/Er/Si/SiO₂/Si structure was analysed by means of cross‐sectional transmission electron microscopy. The Si grains/interlayer formed at the interface and the presence of Si grains within the Er‐related layer constitute proof that Si reacts with Er in the presence of a Pt top layer in the temperature range 450–600 °C. The process of silicide formation in the Pt/Er/Si structure differs from that in the Er/Si structure. At 600 °C, the Pt top layer vanishes and a (Pt–Er)Si_x system is formed.     

New pathways for improved quantification of energy‐dispersive X‐ray spectra of semiconductors with multiple X‐ray lines from thin foils investigated in transmission electron microscopy

Theoretical approaches to quantify the chemical composition of bulk and thin‐layer specimens using energy‐dispersive X‐ray spectroscopy in a transmission electron microscope are compared to experiments investigating (In)GaAs and Si(Ge) semiconductors. Absorption correctors can be improved by varying the take‐off angle to determine the depth of features within the foil or the samples thickness, or by definition of effective k‐factors that can be obtained from plots of k‐factors versus foil thickness or, preferably, versus the K/L intensity ratio for a suitable element. The latter procedure yields plots of self‐consistent absorption corrections that can be used to determine the chemical composition, iteratively for SiGe using a set of calibration curves or directly from a single calibration curve for InGaAs, for single X‐ray spectra without knowledge of sample thickness, density or mass absorption coefficients.     

Moving EM: the Rapid Transfer System as a new tool for correlative light and electron microscopy and high throughput for high-pressure freezing

In this paper, the Rapid Transfer System (RTS), an attachment to the Leica EMPACT2 high‐pressure freezer, is described as a new tool for special applications within the cryofixation field. The RTS is an automated system that allows for fast processing of samples (<5 s) that make it possible for the first time to use high‐pressure freezing in combination with high time resolution correlative light and electron microscopy. In addition, with a working cycle of 30 s this rapid turn over time allows one to acquire more samples of biopsy material before it deteriorates than with other HPF machines with longer cycle times. With the use of the RTS it was possible to obtain three samples each of four different tissues in 6 min. Together with the finding that 90% of samples of cells grown on sapphire discs were well frozen, the RTS was both fast and reliable. Most important, together with other newly developed accessories, the RTS made it possible to capture specific events occurring live in the cell as observed by light microscopy, to cryofix that sample/event within 4 s, and then to analyze that event at high resolution in the electron microscope with excellent preservation of ultra‐structure. These developments should give us the tools to unravel intracellular processes that can be observed by live cell imaging but are too rare or fast to be picked up by routine EM methods or where the history of a structure is necessary to be able to discern its nature.     

Quantitative and reliable in vitro method combining scanning electron microscopy and image analysis for the screening of osteotropic modulators

The increased generation and up-regulated activity of bone resorbing cells (osteoclasts) play a part in the impairment of bone remodeling in many bone diseases. Numerous drugs (bisphosphonates, calcitonin, selective estrogen receptor modulators) have been proposed to inhibit this increased osteoclastic activity. In this report, we describe a pit resorption assay quantified by scanning electron microscopy coupled with image analysis. Total rabbit bone cells with large numbers of osteoclasts were cultured on dentin slices. The whole surface of the dentin slice was scanned and both the number of resorption pits and the total resorbed surface area were measured. Resorption pits appeared at 48 h and increased gradually up to 96 h. Despite the observation of a strong correlation between the total resorption area and the number of pits, we suggest that area measurement is the most relevant marker for osteoclastic activity. Osteotropic factors stimulating or inhibiting osteoclastic activity were used to test the variations in resorption activity as measured with our method. This reproducible and sensitive quantitative method is a valuable tool for screening for osteoclastic inhibitors and, more generally, for investigating bone modulators.     

Videodensitometric analysis of electron spectroscopic micrographs — a tool for detection of biologically relevant elements with high resolution

Electron energy-loss spectroscopic imaging (ESI) yields high-resolution, element-sensitive images. However, ESI suffers from difficulties in distinguishing element-specific and background contributions. New methods have therefore been introduced which use grey-level measurements in micrographic images for a more accurate detection of element distributions. A videodensitometric method allowed the detection of low phosphorus levels in axoplasmic neurofilaments of squid giant axons. Here we further verify these results by investigating the relationship of videodensitometry and electron energy-loss spectroscopy (EELS), particularly considering the peculiarities of these methods in terms of automatic background correction and representation of the results. Six biological specimens and two nonbiological specimens were examined both by EELS and by videodensitometry. In all cases comparable results were obtained. The overlapping P_L2,3 and S_L2,3 ionization edges could clearly be recognized individually by both methods, and controls showed that mass density variations within the specimens did not impair elemental analysis. Additional evidence supporting the detection of phosphorylation sites in squid neurofilaments was obtained in both EELS and videodensitometric measurements of neurofilament-enriched pellets and of aggregated axoplasmic particles. Thus, videodensitometry appears to be a useful tool for an improved exploration of the full imaging capabilities of energy filtering electron microscopy.     

Backscattered electron image of osmium‐impregnated/macerated tissues as a novel technique for identifying the cis‐face of the Golgi apparatus by high‐resolution scanning electron microscopy

The osmium maceration method with scanning electron microscopy (SEM) enabled to demonstrate directly the three‐dimensional (3D) structure of membranous cell organelles. However, the polarity of the Golgi apparatus (that is, the cis–trans axis) can hardly be determined by SEM alone, because there is no appropriate immunocytochemical method for specific labelling of its cis‐ or trans‐faces. In the present study, we used the osmium impregnation method, which forms deposits of reduced osmium exclusively in the cis‐Golgi elements, for preparation of specimens for SEM. The newly developed procedure combining osmium impregnation with subsequent osmium maceration specifically visualised the cis‐elements of the Golgi apparatus, with osmium deposits that were clearly detected by backscattered electron‐mode SEM. Prolonged osmication by osmium impregnation (2% OsO₄ solution at 40°C for 40 h) and osmium maceration (0.1% OsO₄ solution at 20°C for 24 h) did not significantly impair the 3D ultrastructure of the membranous cell organelles, including the Golgi apparatus. This novel preparation method enabled us to determine the polarity of the Golgi apparatus with enough information about the surrounding 3D ultrastructure by SEM, and will contribute to our understanding of the global organisation of the entire Golgi apparatus in various differentiated cells.     

Confocal microscopy of FM4-64 as a tool for analysing endocytosis and vesicle trafficking in living fungal hyphae

Confocal microscopy of amphiphilic styryl dyes has been used to investigate endocytosis and vesicle trafficking in living fungal hyphae. Hyphae were treated with FM4-64, FM1-43 or TMA-DPH, three of the most commonly used membrane-selective dyes reported as markers of endocytosis. All three dyes were rapidly internalized within hyphae. FM4-64 was found best for imaging the dynamic changes in size, morphology and position of the apical vesicle cluster within growing hyphal tips because of its staining pattern, greater photostability and low cytotoxicity. FM4-64 was taken up into both the apical and subapical compartments of living hyphae in a time-dependent manner. The pattern of stain distribution was broadly similar in a range of fungal species tested ( Aspergillus nidulans, Botrytis cinerea, Magnaporthe grisea, Neurospora crassa , Phycomyces blakesleeanus, Puccinia graminis, Rhizoctonia solani, Sclerotinia sclerotiorum and Trichoderma viride ). With time, FM4-64 was internalized from the plasma membrane appearing in structures corresponding to putative endosomes, the apical vesicle cluster, the vacuolar membrane and mitochondria. These observations are consistent with dye internalization by endocytosis. A speculative model of the vesicle trafficking network within growing hyphae is presented.     

KSpaceNavigator as a tool for computer-assisted sample tilting in high-resolution imaging, tomography and defect analysis

This article describes a novel software tool, the KSpaceNavigator, which combines sample stage and crystallographic coordinates in a control sphere. It also provides simulated kinematic diffraction spot patterns, Kikuchi line patterns and a unit cell view in real time, thus allowing intuitive and transparent navigation in reciprocal space. By the overlay of experimental data with the simulations and some interactive alignment algorithms, zone axis orientations of the sample can be accessed quickly and with great ease. The software can be configured to work with any double-tilt or tilt–rotation stage and overcomes nonlinearities in existing goniometers by lookup tables. A subroutine for matching the polyhedral shape of a nanoparticle assists with 3D analysis and modeling. The new possibilities are demonstrated with the case of a faceted BaTiO₃ nanoparticle, which is tilted into three low-index zone axes using the piezo-controlled TEAM stage, and with a multiply twinned tetrahedral Ge precipitate in Al, which is tilted into four equivalent zone axes using a conventional double-tilt stage. Applications to other experimental scenarios are also outlined.